I think you have to split the file into 2 MFS returns then use the wife's MFS return to complete the FBAR for her...personally I just go here and do it outside of ProSeries
Not sure about ProSeries but it's like Lacerte/PTO, you can e-file just the spouse's FBAR by checking the box for Spouse and not notating any joint account holder for that account.
Just to add to Lisa's post, the link she referenced is for direct filing by taxpayers. As a tax preparer, you will need to enroll as a BSA E-Filer. Once your account is set up, if you don't already have one, you can then log into the portal using your account, prepare the FBAR, and submit it from the website.
Still an AllStar